to cite kids selling their rings as NOT a clean program then I can cite DUI's fights, improper benefits at BYU as well for not clean.... and BM's win percentage is soooo over inflated by a crappy schedule it ain't funny... see recent slight upticks in schedule strength and on field results as examples of his win percentage not being great.
I haven't gone through the entire history of CFB, but I'm certain there are plenty more. Was Paterno fired? He ran a clean program.